title: mouse_activating_frame+3_unsorted

data_processing:
library strategy: ORFtag
First, iPCR reads from sorted and background (non-selected, input) samples were trimmed using Trim galore (v0.6.0) with default parameters to remove Illumina adapters. Then, trimmed reads were aligned to the mm10 version of the mouse genome using bowtie220 (v2.3.4.2) with default parameters (for paired-end sequenced samples, only first mate reads were considered), before removal of duplicated and low mapping quality reads (mapq<=30) using samtools (v1.9)21. Mapped insertions were assigned to the closest downstream exon junction – with a maximum distance of 200kb – based on GENCODE annotations of the mouse genome (vM25). Finally, insertion counts were aggregated per gene. Of note, only exons from protein-coding transcripts were considered, except for the first exon of each transcript, which does not contain splicing acceptor sites. Consequently, intronless genes – for which none of the isoforms contain a spliced intron – were not considered.
Finally, genes showing significantly more insertions in sorted samples compared to unsorted samples (using the same cassette) were identified using one-tailed fisher's exact test (alternative= "greater"). Of note, only genes with at least 3 unique insertions in sorted samples were considered. Obtained p-values were corrected for multiple testing using the FDR method and genes showing an FDR<0.001 and a log2 Odd Ratio≥1 were classified as hits.
Assembly: mm10
Supplementary files format and content: counts_same_strand files contains the genomic coordinates of all the insertions that were found in the sample, and the id of the assigned gene. In addition, the distance between the insertion and the exon that was used for assignment, as well as its position (number) inside the gene, are reported.
Supplementary files format and content: counts_rev_strand is similar to the previous (counts_same_strand) file, but reports the assignment of reversed insetions. Used to compute strand bias.
Supplementary files format and content: The sorted_vs_unsorted.txt files contain, for each gene, the unique insertions enrichment in sorted vs unsorted samples (log2OR) with the associated FDR (padj). In this study, all genes with a FDR<0.001 were considered as hits (see "hit" column).

treatment_protocol: The ORFtag viral constructs were derived from the ecotropic Retro-EGT construct13 that includes the sequence features necessary for the inverse-PCR protocol (detailed below and in Extended Data Fig. 1). Furthermore, the construct feature a constitutively active PGK promoter that drives the expression of a NeoR resistance gene separated from a tag by the IRES sequence. The tag contained either TetR with an N-terminally located nuclear localization signal (Activator screen, Repressor screen; Addgene, this study) or LambdaN domain (PTGR screen; Addgene, this study). Additionally, the tag includes a 2x GGGS-linker followed by the BC2-tag and 3xFLAG-tag. Finally, the ORFtag construct contains a consensus splice donor motif (GT) followed by a segment of the Hprt intron (chrX:53020400-53020556 +, mm10). To ensure tagging of genes in all three possible coding frames, three variants of the constructs were used that contain either 0, 1 or 2 additional nucleotides upstream of the consensus splice motif (GT), resulting in the following sequence: AAG-CAG-GT (frame 1), AAG-G-CAG-GT (frame 2) or AAG-GC-CAG-GT (frame 3) where AAG represents the last codon of the 3xFLAG-tag.


title: Patient6, post Treatment, TCRseq

status: Public on May 10 2024

type: SRA

city: Berlin

first: Artur

last: Wilhelm

address: Virchowweg 11

department: Rheumatology and clinical immunology

country: Germany

institute: Charite Berlin

description: 10x Genomics

library_source: other

data_processing:
Demultiplexing, barcode processin, gene counting and clonotype calling was performed using the cellranger multi pipeline v.7.0.0.
Assembly: hg38
Supplementary files format and content: Tab seperated matrix, gene and barcode files
Library strategy: TCR-Seq

molecule: other

organism: Homo sapiens

source_name: Blood

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were separated using SepMate™-50 (StemCell) and Ficoll-Paque gradient centrifugation following the manufacturer's protocol.
libraries were constructed using the Chromium Next GEM Single cell 5´Reagent Kits v2 (10 X Genomics)

tag: tissue

value: Blood

tag: cell type

value: T cells

tag: treatment

value: post anti CD19 CART-cell therapy


title: Patient6, pre Treatment, TCRseq

description: 10x Genomics

value: pre anti CD19 CART-cell therapy


title: mouse_activating_frame+2_unsorted

city: Vienna

first: Alexander

last: Stark

address: Campus-Vienna-Biocenter 1

country: Austria

institute: The Research Institute of Molecular Pathology (IMP)

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: mESC

growth_protocol: All experiments presented here were carried out in diploid mouse embryonic stem cells (mESCs) that were derived from originally haploid HMSc2 termed AN3-1213. The mESCs were cultivated without feeders in high-glucose-DMEM (Sigma-Aldrich) supplemented with 13.5% fetal bovine serum (Sigma-Aldrich), 2 mM L-glutamine (Sigma-Aldrich), 1x Penicillin-Streptomycin (Sigma-Aldrich), 1x MEM non-essential amino acid solution (Gibco), 1mM sodium pyruvate (Sigma-Aldrich), 50 mM β-mercaptoethanol (Merck) and in-house produced recombinant LIF. Virus packaging cell lines, Lenti-X 293T (Takara) and PlatinumE (Cell Biolabs), were grown according to the manufacturer’s instructions. All cell lines were cultured at 37°C and 5% CO2 and regularly tested for mycoplasma contamination.

extract_protocol:
Genomic locations of ORFtag integrations were mapped using modified inverse-PCR followed by next generation sequencing (iPCR-NGS) protocol8. Genomic DNA was prepared by lysing cell pellets in lysis buffer (10 mM Tris-HCl pH 8.0, 5 mM EDTA, 100 mM NaCl, 1% SDS, 0.5 mg/ml proteinase K) at 55°C overnight. Following a 2-hour RNase A treatment (Qiagen, 100 mg/ml, 1:1,000 dilution) at 37°C, two extractions using phenol:chloroform:isoamyl alcohol and one extraction using chloroform:isoamyl alcohol were carried out.
The samples then underwent two separate digestion reactions (with up to 4 µg of genomic DNA) using NlaIII and MseI enzymes (NEB) at 37°C overnight, followed by purification using a Monarch PCR&DNA Cleanup Kit (NEB). Ring-ligation was carried out using T4 DNA ligase (NEB) at 16 °C overnight, followed by heat-inactivation (65°C, 15 min) and linearization using SbfI-HF (NEB) at 37°C for 2 h. The digests were then purified using a Monarch PCR&DNA Cleanup Kit (NEB) and amplified using firstly a nested PCR reaction with KAPA HiFi HotStart ReadyMix (Roche), and a specific primer pair (TGCAGGACCGGACGTGACTGGAGTTC*A, TGCAGGACGATGAGCAGAGCCAGAACC*A) for 16 cycles. After cleanup with AMPure XP Reagent (Beckman Coulter, 1:1 ratio beads:PCR), iPCR amplification was carried out with KAPA HiFi HotStart ReadyMix (Roche), and a specific primer pair (AATGATACGGCGACCACCGAGATCTACACGAGCCAGAACCAGAAGGAACTTGA*C, CAAGCAGAAGACGGCATACGAGAT [custom-barcode] GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT) for 18 cycles. Afterwards, amplified libraries were size selected for a range of 400-800 bp using SPRIselect beads (Beckman Coulter). NGS was performed on an Illumina NextSeq550 or llumina HiSeq 2500 sequencer according to the manufacturers’ protocols with custom first-read primer (1:1 mix of GAGTGATTGACTACCCGTCAGCGGGGGTCTTTCA and TGAGTGATTGACTACCCACGACGGGGGTCTTTCA).

tag: cell line

value: mESC

tag: genotype

value: wild-type cells with 7xTetO-pMYLPF-Puro-IRES-GFP reporter integrated into the expression-stable locus on Chr15, clonal cell line


title: cord blood-derived megakaryocytes, 8 h CA treated, biological rep 1

type: RNA

city: Philadelphia

first: Christopher

last: Thom

state: PA

address: 3501 Civic Center Blvd

country: USA

institute: Children's Hospital of Philadelphia

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: R/Bioconductor (oligo, limma, affycoretools) were used in the initial processing.

label: biotion

molecule: total RNA

source_name: Umbilical cord blood-derived megakaryocytes

label_protocol: Affymetrix protocol

extract_protocol: Total RNA was isolated using commercially available kits.

tag: treatment group

value: 8h CA


title: mouse_activating_frame+1_unsorted


title: Spinal cord, Uninjured, P6981_1001

city: Solna

first: Christian

last: Göritz

address: Solnavägen 9

department: CMB

country: Sweden

institute: Karolinska Institutet

library_source: transcriptomic

data_processing:
Clustering was done by 'cBot' and samples were sequenced on Illumina HiSeq2500 (HiSeq Control Software 2.2.58/RTA 1.18.64) with a 1x51 setup using 'HiSeq SBS Kit v4' chemistry. The Bcl to FastQ conversion was performed using bcl2fastq from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+. Mus musculus, GRCm38 was used as reference genome.   We used a single-cell RNA sequencing snakemake workflow (“lts_workflows_sm_scrnaseq”) for alignment, quantification and quality control using resources as follows: The reads were aligned to the mouse (mm10) genome using STAR 2.5.3a (Dobin et al., 2013) and transcripts quantified in terms of Reads Per Kilobase of transcript per Million mapped reads (RPKM) using rpkmforgenes v1.0.1  (Ramsköld et al., 2009) and RSEM to estimate gene and isoform expression levels v1.2.28  (Li and Dewey, 2011). RSeQC V2.6.4  (Wang et al., 2012) Multiqc v0.9.1 were used for quality control. To filter out low quality libraries the following filtering criteria for quality control were applied: star_Uniquely mapped: < mean - 2 sd, gene_detection : > mean - 2 sd & < mean + 2 sd, count_gene : < mean - 2 sd, gene_correlation_max : < mean - 2 sd. Cells that failed for 2 of the criteria were filtered out (25 cells, 2.89% of 864, the total number of cells).
Assembly: mm10
Supplementary files format and content: rpkmforgenes_counts.tab
Supplementary files format and content: 170706_sampleinfo_scs.csv

source_name: Spinal cord

extract_protocol:
Preparation of single-cell cell suspension and myelin removal was adapted from previously published protocols (Lovatt et al., 2007; Orre et al., 2014). In summary, the procedure was: 5 days after spinal cord crush injury, animals were euthanized by intraperitoneal injection of sodium pentobarbital (200mg/Kg, 100ul i.p., APL) and transcardially perfused with cold Hank's Balanced Salt Solution without calcium or magnesium (HBSS) (Invitrogen). The vertebral column was immediately removed to cold HBSS, the spinal cord was carefully dissected out of the vertebrae and the crush injury segment was separated from the uninjured spinal cord and treated separately hereafter. After removal of the outer meningeal layers, the tissue was dissociated mechanically with a razor blade on a glass petri dish and immediately transferred to cold HBSS. Followed by enzymatic digestion with papain at a final concentration of 8 U/mL with 80 Kunitz units/mL DNase I (Sigma-Aldrich, D4263) in Ca2+/Mg2+-free piperazine-N,N′-bis(2-ethanesulfonic acid) (PIPES)/cysteine -based buffer, pH 7.4, for 40min at 37°C, 350rpm on a ThermoMixer® (Eppendorf). The tissue was carefully triturated and incubated for additional 5min. The cell suspension was passed through a 70μmCell Strainer (Corning), washed with Minimum Essential Media (MEM) with 1% bovine serum albumin (BSA) and spun down at 200g for 5min at 4°C. The cells were resuspended in MEM and centrifuged over a 90% Percoll gradient (GE Healthcare, 17-0891-01) at 250g for 15min at 4°C. Cells in the lipid layer and below were diluted 5 times in MEM with 1% BSA and spun in a 15mL tube at 250g for 10min at 4°C. All supernatant including the lipid layer were carefully removed and the pellet resuspended in cold MACS Buffer and magnetic Myelin removal beads (Miltenyi biotech, 130-096-433) and incubated for 15min at 4°C. The cells were washed and run over MACS MS columns (Miltenyi biotech, 130-042-201) on a magnetic stand according to the manufacturer’s instructions. The flow through cells were collected, spun down and resuspended in FACS buffer. The single cell suspensions derived from normal spinal cord and injury segments were subject to FACS (fluorescence activated cell sorting) into GLAST-CreER-tomato+/Pdgfrb-eGFP+ double positive and Pdgfrb-eGFP+ single cells, into 96-well plates with Cell lysis buffer (Clonetech, 635013) and frozen to -80°C. Cell sorting was performed on a FACSAria III Cell Sorter system (BD Biosciences). Singlet discrimination was performed using plots for forward scatter (FSC-A versus FSC-H) and side scatter (SSC-W versus SSC-H), dead cells were excluded by SYTOX Blue Dead Cell Stain (ThermoFisher Scientific, S34857).
Single cells were processed to cDNA libraries according to the Smart-Seq2 protocol  (Picelli et al. 2014). Tn5 tagmentation was performed using the Nextera XT DNA library Preparation Kit (Illumina, FC-131-1002) using dual indexes (i7 and i5).

value: Spinal cord

value: Perivascular cells

tag: Sex

value: female

tag: sorted population

value: EGFP+; tdTomato-


title: Patient5, post Treatment, TCRseq

description: 10x Genomics


title: mouse_activating_frame+1_sorted


title: Spinal cord

data_processing:
see  Smart-Seq3express protocol  (Hagemann-Jensen et al. 2022)
Assembly: mm10
Supplementary files format and content: NN_Glast_B_d0d3d5_count_matrix.csv
Supplementary files format and content: NN_sampleinfo_scs.csv

extract_protocol:
Preparation of single-cell cell suspensions and myelin removal was  performed using adult brain dissociation kit (130-107-677, Miltenyi), followed by Smart-seq 3 express library preparation protocol. In summary, uninjured, and 3 days and 5 days after spinal cord crush GLAST-CreERT2;R26R-tdTomato;Pdgfrb-eGFP animals were euthanized by intraperitoneal injection of sodium pentobarbital and transcardially perfused with cold Hank's Balanced Salt Solution without calcium or magnesium (HBSS) (Invitrogen). The spinal cord was carefully dissected out of the vertebrae and the crush injury segment was separated from the uninjured spinal cord tissue and treated separately hereafter. After removal of the outer meningeal layers, the tissue was mechanically dissociated with a razor blade on a glass Petri dish and immediately transferred to cold HBSS. This step was followed by enzymatic digestion. Following dissociation cell pellets were resuspended in cold MACS buffer and magnetic myelin removal beads (Miltenyi Biotech, 130-096-433) and incubated for 15 min at 4°C. The cells were washed and run over MACS MS columns (Miltenyi Biotech, 130-042-201) on a magnetic stand according to the manufacturer’s instructions. The cells in the flow through were collected, spun down, resuspended in PBS and kept on ice until further processing. The single-cell suspensions generated from GLAST-CreERT2;R26R-tdTomato;Pdgfrb-eGFP animals were subjected to fluorescence activated cell sorting (FACS). Based on reporter gene expression, tdTomato+EGFP+ and tdTomato-EGFP+ cells were collected into 384 plates with Smart-seq 3 express lysis buffer mix, followed by a brief centrifugation (1 min, 1500 rpm) and stored at -80 °C until further processing. Cell sorting was performed on a FACSAria III Cell Sorter (BD Biosciences). Singlet discrimination was performed using plots for forward scatter (FSC-A versus FSC-H) and side scatter (SSC-W versus SSC-H), and dead cells were excluded by SYTOX Blue Dead Cell Stain (ThermoFisher Scientific, S34857).
Single cells were processed to cDNA libraries according to the Smart-Seq3express protocol  (Hagemann-Jensen et al. 2022).


title: Patient5, pre Treatment, TCRseq

description: 10x Genomics


title: Patient4, pre Treatment, TCRseq

description: 10x Genomics


title: Patient4, post Treatment, TCRseq

description: 10x Genomics


title: cord blood-derived megakaryocytes, 4 h CA treated, biological rep 1

value: Umbilical cord blood-derived megakaryocytes

value: 4h CA


title: cord blood-derived megakaryocytes, 4 h CA treated, biological rep 2


title: mouse_activating_frame+2_sorted


title: SKmel147 YL1sh84, H4ac ChIPseq

city: New York

first: Sina

last: Jostes

state: NY

address: 1470 Madison Avenue

institute: Icahn School of Medicine at Mt Sinai

description: 1% Formaldehyde

data_processing:
ChIP reads were aligned to the human reference genome GRCh37/hg19 using Bowtie (version 1.1.2) (Langmead et al. 2009) with parameters –l 50 –n 2 –S --best –k 1 –m 1 for ZNHIT1 and YL1 or –l 65 –n 2 –best –k 1 –m 1 for H4ac.
Duplicate reads were removed with PICARD (version 2.2.4) (Broad Institute).
Binary alignment map (BAM) files were generated with samtools v1.9 (Li et al., 2009)
Bigwig files were generated from BAM files using deepTools bamCoverage (version 2.4.1) with parameters –normalizeUsingRPKM –binsize 10.
Significant peaks were identified using MACS2 (version 2.1.0) (Zhang et al. 2008) where q-value cut-offs were determined post-hoc, testing several q-values based on signal to background ratio. YL1 and ZNHIT1 peaks were called against matching input control with parameters --nomodel –s 75 --keep-dup 2 -q 0.005 or -q 0.05 (for ZHNIT1 ChIP). For the H4ac ChIP-seq the bam files of 2 control and 2 knockdown samples (shSCR 2x, and YL1 sh30 and YL1 sh84) were concatenated using samtools merge to generate ‘master’ bam files. Significant peaks were called on ‘master’ bam files and matching input controls using MACS2 for narrow peaks with -q 1e-10. Peaks in ENCODE blacklisted regions were removed.
Assembly: GRCh37/hg19
Supplementary files format and content: bigwig

growth_protocol: DMEM, 10% FBS, 1% P/S

extract_protocol:
For YL1 and H4ac ChIP, SK-MEL-147 cells were cross-linked with 1% Formaldehyde for 10 min at room temperature. For ZNHIT1 ChIP, SK-MEL-147 cells were were double cross-linked with 0.25 M disuccinimidyl glutarate (DSG) for 45 min, followed with 1% formaldehyde for 10 min. ChIP was performed  as previously described (Fontanals-Cirera B, Hasson D, Vardabasso C, Di Micco R et al. Harnessing BET Inhibitor Sensitivity Reveals AMIGO2 as a Melanoma Survival Gene. Mol Cell 2017 Nov 16;68(4):731-744.e9)
Libraries for ChIP-seq were done as previously described  (Fontanals-Cirera B, Hasson D, Vardabasso C, Di Micco R et al. Harnessing BET Inhibitor Sensitivity Reveals AMIGO2 as a Melanoma Survival Gene. Mol Cell 2017 Nov 16;68(4):731-744.e9)

treatment_protocol: For H4ac ChIP-seq, cells were harvested 6 days post infection with shSCR or shYL1 (sh30, sh84)

value: YL1 KD

tag: antibody


title: cord blood-derived megakaryocytes, DMSO control, biological rep 3

value: DMSO


title: cord blood-derived megakaryocytes, 4 h CA treated, biological rep 3


title: cord blood-derived megakaryocytes, DMSO control, biological rep 1


title: cord blood-derived megakaryocytes, DMSO control, biological rep 2


title: Patient3, post Treatment, TCRseq

description: 10x Genomics


title: SKmel147 YL1sh30, H4ac ChIPseq

description: 1% Formaldehyde


title: Patient3, pre Treatment, TCRseq

description: 10x Genomics


title: SKmel147 shSCR2, H4ac ChIPseq

description: 1% Formaldehyde

value: shSCR


title: E2Rln_2hr_Replicate2

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

data_processing:
The RNA-seq reads were aligned to the mm10 mouse reference genome using tophat2 .
Mapped reads were sorted and captured in bam files for further downstream analysis of differential gene expression and  bigwig files were generated to for presentation as browser tracks using custom R scripts.
Assembly: mm10
Supplementary files format and content: BigWig

source_name: mouse myoterium

growth_protocol: Samples were collected for each of the four treatment time points (vehicle, E2, Rln, and E2+Rln) from ovariectomized mice treated for 2 hours.

extract_protocol:
Total RNA was isolated from myometrial tissue using a RNeasy Plus Mini Kit (Qiagen), according to manufacturer’s instructions.  Myometrial tissue was homogenized in RLT buffer with a cooled blade homogenizer (Power Gen25; Fisher). The samples were centrifuged to remove debris and passed through a gDNA eliminator column, followed by RNA binding column. After multiple washes, total RNA was eluted with RNase-free water.  The eluted RNA was assayed for quality by electrophoresis (Agilent Technologies, Santa Clara, CA, USA).  Only samples with RIN values greater than 8 were included for RNA-sequencing.
RNA-seq libraries from mouse myometrial tissue were prepared as follows using a protocol described previously (Zhong et al., 2011).  Briefly, biological replicates were generated by pooling 1.5 mg of total RNA from five animals for a total of 7.5 mg of total RNA per replicate.  A total of ten animals were used for each treatment time point.  Polyadenylated RNA was isolated from total RNA using Oligo(dT)25 Dynabeads (Invitrogen) and reverse transcribed using SuperScript III Reverse Transcriptase (Invitrogen).  Second strand synthesis was performed using DNA polymerase I.  Complementary DNA ends were repaired, tailed with dATP, and ligated with barcode adapters for Illumina sequencing platform.  Ligated libraries were selected for average size 270 bp, PCR amplified for 9 cycles, and sequenced on an Illumina NextSeq 500 in a 75 bp single-end format in the McDermott Center Next Generation Sequencing Core at UT Southwestern Medical Center to a total read count of ~40 M per condition.

value: mouse myoterium

value: myometrium tissue treated with E2 and Rln


title: Rln_2hr_Replicate2

value: myometrium tissue treated with 80ug/ml of Rln


title: Patient2, pre Treatment, TCRseq

description: 10x Genomics

value: Blood

value: T cells


title: SKmel147 shSCR, H4ac ChIPseq

description: 1% Formaldehyde


title: mouse_activating_frame+3_sorted

value: mESC


title: SKmel147, YL1 ChIPseq

description: DSG + 1% Formaldehyde

value: Parental line


title: Patient1, post Treatment, TCRseq

description: 10x Genomics

value: post anti CD19 CART-cell therapy


title: Patient2, post Treatment, TCRseq

description: 10x Genomics


title: E2Rln_2hr_Replicate1


title: SK-MEL-147 cells, H2A.Z.2 knockdown sh37, 6 days, replicate 2

description:
shH2AZ2_vs_SCR_d6.csv
shH2A.Z.2-sh37-6d-rep2
H2AZ1_H2AZ2_d6_normcounts.txt

data_processing:
Reads were aligned to the human reference genome (hg19/GRCh37.p13) with STAR (Dobin et al. 2013) (version 2.6.0.c) using the parameters --runMode alignReads --sjdbOverhang 100 --outFilterMultimapNmax 10 --outFilterMismatchNmax 10 --
Following, featureCounts from the Rsubread (Liao et al. 2019) (version 2.4.3) R package was used to assign reads to coding genes.
Assigned reads were then normalized and differentially expressed genes were identified using the R package DEseq2 (version 1.30.1) (Love et al. 2014)
Genes were considered expressed if the sum of raw counts was >10 for any given gene. Differentially expressed genes were called using an adjusted p value <= 0.05 and log2FC >= 0.75 or <= -0.75.
YL1, SRCAP and P400 knockdowns were compared to SCR controls rep1-6. H2A.Z.1 and H2A.Z.2 knockdowns were compared to H2A.Z shSCR controls rep 1 and rep2.
Assembly: hg19
Supplementary files format and content: CSV files with lists of differentially expressed genes

molecule: polyA RNA

growth_protocol: SK-MEL-147 were cultured in DMEM supplemented with 10% FBS, 100 IU of penicillin and 100 μg/mL of streptomycin

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) and the quality of RNA samples was assessed on a 2100 Agilent Bioanalyzer
mRNA was extracted from 2 ug of total RNA per sample using NEXTFLEX® Poly(A) Beads 2.0 (Perkin Elmer, Austin, Texas, USA). Libraries were prepared from mRNA samples using NEXTFLEX® Rapid Directional RNA-seq Kit 2.0 (Perkin Elmer, Austin, Texas, USA). Quality of library preparation was assessed on a 2100 Agilent Bioanalyzer

treatment_protocol: 5x10^5 cells were seeded into 10-cm plates and infected with shRNA virus the following day. Next morning, cells were washed twice with PBS and then selected in DMEM medium containing puromycin (2 mg/mL) for 24 hours.

value: Melanoma

value: H2A.Z.2 knockdown


title: E2_2hr_Replicate2

value: myometrium tissue treated with 2.5ug/ml of E2


title: SKmel147, ZNHIT1 ChIPseq

description: DSG + 1% Formaldehyde


title: Patient1, pre Treatment, TCRseq

description: 10x Genomics

value: pre anti CD19 CART-cell therapy


title: E2_2hr_Replicate1


title: Patient7, pre Treatment, scRNAseq

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcode processin, gene counting and clonotype calling was performed using the cellranger multi pipeline v.7.0.0.
Assembly: hg38
Supplementary files format and content: Tab seperated matrix, gene and barcode files

value: PBMCs


title: Patient7, post Treatment, scRNAseq

description: 10x Genomics


title: SK-MEL-147 cells, H2A.Z.1 knockdown sh83, 6 days, replicate 2

description:
shH2AZ1_vs_SCR_d6.csv
shH2A.Z.1-sh83--6d-rep2
H2AZ1_H2AZ2_d6_normcounts.txt

value: H2A.Z.1 knockdown


title: Vehicle_Replicate2

value: myometrium tissue treated with saline


title: Vehicle_Replicate1


title: Patient6, post Treatment, scRNAseq

description: 10x Genomics


title: SK-MEL-147 cells, H2A.Z.1 knockdown sh83, 6 days, replicate 1

description:
shH2AZ1_vs_SCR_d6.csv
shH2A.Z.1-sh83-6d-rep1
H2AZ1_H2AZ2_d6_normcounts.txt


title: Patient6, pre Treatment, scRNAseq

description: 10x Genomics


title: SK-MEL-147 cells, H2AZ shSCR control, 6 days, replicate 2

description:
SCR-H2AZ-6d-rep2
H2AZ1_H2AZ2_d6_normcounts.txt

value: shSCR knockdown


title: Nanocapsule treated, replicate 2, scRNAseq

city: Los Angeles

first: Jeffrey

last: Harding

state: CA

address: 405 Hilgard Avenue

institute: University of California Los Angeles

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10

source_name: Tumor

extract_protocol: Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Cancer cells

value: Tumor

tag: strain

tag: age

value: 6-8 weeks old

value: Nanocapsule


title: SK-MEL-147 cells, H2A.Z.2 knockdown sh37, 6 days, replicate 1

description:
shH2AZ2_vs_SCR_d6.csv
shH2A.Z.2-sh37-6d-rep1
H2AZ1_H2AZ2_d6_normcounts.txt


title: Rln_2hr_Replicate1

value: mouse myoterium

value: myometrium tissue treated with 80ug/ml of Rln


title: SK-MEL-147 cells, H2AZ shSCR control, 6 days, replicate 1

description:
SCR-H2AZ-6d-rep1
H2AZ1_H2AZ2_d6_normcounts.txt


title: Patient5, post Treatment, scRNAseq

description: 10x Genomics

value: Blood


title: Control, replicate 2, scRNAseq

description: 10x Genomics

value: Control


title: Patient5, pre Treatment, scRNAseq

description: 10x Genomics


title: SK-MEL-147 cells, P400 knockdown sh62, 6 days, replicate 2

description:
shP400_vs_SCR_d6.csv
shP400-sh62-6d-rep2
YL1_SRCAP_P400_d6_normcounts.txt

value: P400 knockdown


title: Control, replicate 1, scRNAseq

description: 10x Genomics


title: SK-MEL-147 cells, P400 knockdown sh62, 6 days, replicate 1

description:
shP400_vs_SCR_d6.csv
shP400-sh62-6d-rep1
YL1_SRCAP_P400_d6_normcounts.txt

value: Melanoma


title: Patient4, pre Treatment, scRNAseq

description: 10x Genomics


title: lung_WT_ATR240.2

city: RTP

first: Huiling

last: Li

state: NC

address: 111 T.W. Alexander Dr

institute: NIEHS

data_processing:
Adapter sequences were trimmed from reads using Cutadapt (Martin 2011) and low quality reads were removed from analysis using Sickle 1.33 (Joshi et al. 2011).
RNA-seq reads were mapped to the mouse reference genome (mm39) using STAR (Dobin et al., 2013) with default parameters.
Gene counts were generated using Salmon (Patro et al. 2017) and transformed with log2(1 + x).
Differential expression analysis was performed on aggregated gene pseudocounts using limma-voom 3.42.2 (Law et al. 2014).
Genome_build: mm39
Supplementary files format and content: Processed data represents Salmon transcript (tx) or gene (gene) pseudocounts in tab-delimited format.

source_name: mouse wildtype lung

extract_protocol:
Adam19 WT and KO mice (n=3 per genotype per tissue) were euthanized with an overdose of sodium pentobarbital (200 mg/kg, i.p. injection) followed by puncture of the diaphragm and vena cava exsanguination. The whole heart and lung were immediately removed and frozen with liquid nitrogen. RNA was isolated from the heart and lung using the RNeasy® Mini Kit (Qiagen, Hilden, Germany).
Illumina Tru-Seq stranded total RNA was used to construct sequencing libraries.

value: lung

value: wildtype

value: male


title: heart_WT_ATR240.2

source_name: mouse wildtype heart

value: heart


title: SK-MEL-147 cells, P400 knockdown sh60, 6 days, replicate 2

description:
shP400_vs_SCR_d6.csv
shP400-sh60-6d-rep2
YL1_SRCAP_P400_d6_normcounts.txt


title: Patient4, post Treatment, scRNAseq

description: 10x Genomics

value: PBMCs

value: post anti CD19 CART-cell therapy


title: lung_Mut_ATR237.3

source_name: mouse Adam19 knockout lung

value: Adam19 knockout


title: SK-MEL-147 cells, P400 knockdown sh60, 6 days, replicate 1

description:
shP400_vs_SCR_d6.csv
shP400-sh60-6d-rep1
YL1_SRCAP_P400_d6_normcounts.txt


title: Patient3, post Treatment, scRNAseq

description: 10x Genomics


title: heart_Mut_ATR237.3

source_name: mouse Adam19 knockout heart


title: SK-MEL-147 cells, shSCR control, 6 days, replicate 6

description:
SCR-P400-6d-rep2
YL1_SRCAP_P400_d6_normcounts.txt

value: shSCR knockdown


title: Patient3, pre Treatment, scRNAseq

description: 10x Genomics

value: pre anti CD19 CART-cell therapy


title: SK-MEL-147 cells, shSCR control, 6 days, replicate 5

description:
SCR-P400-6d-rep1
YL1_SRCAP_P400_d6_normcounts.txt


title: Patient2, post Treatment, scRNAseq

description: 10x Genomics


title: SK-MEL-147 cells, SRCAP knockdown sh29, 6 days, replicate 2

description:
shSRCAP_vs_SCR_d6.csv
shSRCAP-sh29-6d-rep2
YL1_SRCAP_P400_d6_normcounts.txt

value: SRCAP knockdown


title: Patient2, pre Treatment, scRNAseq

description: 10x Genomics


title: heart_Mut_ATR237.2


title: Patient1, post Treatment, scRNAseq

description: 10x Genomics


title: SK-MEL-147 cells, SRCAP knockdown sh29, 6 days, replicate 1

description:
shSRCAP_vs_SCR_d6.csv
shSRCAP-sh29-6d-rep1
YL1_SRCAP_P400_d6_normcounts.txt


title: Patient1, pre Treatment, scRNAseq

description: 10x Genomics


title: lung_Mut_ATR236.4


title: SK-MEL-147 cells, SRCAP knockdown sh30, 6 days, replicate 2

description:
shSRCAP_vs_SCR_d6.csv
shSRCAP-sh30-6d-rep2
YL1_SRCAP_P400_d6_normcounts.txt


title: heart_Mut_ATR236.4


title: SK-MEL-147 cells, SRCAP knockdown sh30, 6 days, replicate 1

description:
shSRCAP_vs_SCR_d6.csv
shSRCAP-sh30-6d-rep1
YL1_SRCAP_P400_d6_normcounts.txt


title: lung_WT_ATR234.2


title: SK-MEL-147 cells, shSCR control, 6 days, replicate 4

description:
SCR-SRCAP-6d-rep2
YL1_SRCAP_P400_d6_normcounts.txt


title: RT00390N snATAC-seq

city: Irvine

first: Jing

last: Zhang

address: University of California, Irvine

institute: University of California, Irvine

library_source: genomic single cell

data_processing:
We first removed the barcodes with the high possibility of being doublets or having poor quality on the snRNA-seq side, using the list of barcodes after Pegasus processing with the subset() function in Signac v.1.5.0. Then, for each sample, we created a chromatin assay object using the CreateChromatinAssay function with other metadata, including fragments, n_counts, and n_frags, properly added. Then, we filtered each sample to keep only cells with a sequencing depth of >1,000 and a TSS enrichment of ≥2. We set the cutoff threshold to 2 due to the fact that post-mortem brain cells tend to have lower quality, especially in terms of the TSS enrichment. Setting a threshold too large (for instance, 4) may result in a dramatic loss of sample size to study. After the dataset was filtered and curated, we used the CallPeaks function in the Signac package to call the peaks. We used the default parameters and Macs2 2.2.6. Then, ATAC count matrices are generated and stored as MTX files along with a barcode list (text file) and a unified peak set (bed file).
For snRNA-seq data portion, in addition to the snATAC-seq QC step, we filter out all potential doublets using doubletdetection package with n_iters = 25, use_phenograph = False, and standard_scaling = True. We then formulate the count matrix as MTX files, plus the list of barcodes (text files) and the gene list (a text file).
Assembly: GRCh38
Supplementary files format and content: Sparse Matrix file, count matrix (normalized for snRNA-seq)
Supplementary files format and content: Text file, barcode list

source_name: post mortem human brain

extract_protocol:
To obtain pure and intact nuclear populations, brain tissues were homogenized by a Dounce homogenizer in an ice-cold isolation buffer containing 2M sucrose. All buffers were ice-cold and all reagents used for nuclear isolation were molecular biology grade unless stated otherwise. A total of 20-30 mg of pulverized tissue was added into 5 ml of ice-cold lysis buffer (320 mM sucrose [Sigma #S0389], 5 mM CaCl2 [Sigma #21115], 3 mM Mg[Ace]2 [Sigma #63052], 10 mM Tris-HCl [pH 8; AmericanBio #AB14043], protease inhibitors without EDTA [Roche #11836170001], 0.1 mM EDTA [AmericanBio #AB00502], RNAse inhibitor [80 U/ml; Roche #03335402001], 1 mM dithiothreitol [DTT; Sigma #43186], and 0.1% TX-100 [v/v; Sigma #T8787]). Reagents DTT, RNAse protector, protease inhibitors, and TX-100 were added immediately before use. The suspension was transferred to a Dounce tissue grinder (15 ml volume, Wheaton #357544, autoclaved, RNAse free, ice-cold) and homogenized with loose and tight pestles, 30 cycles each, with constant pressure and without introduction of air. The homogenate was strained through a 40-µm tube top cell strainer (Corning #352340) pre-wetted with 1 ml isolation buffer (1,800 mM sucrose [Sigma #S0389], 3 mM Mg[Ace]2 [Sigma #63052], 10 mM Tris-HCl [pH 8; AmericanBio #AB14043], protease inhibitors without EDTA [Roche #11836170001], RNAse inhibitor [80 U/ml, Roche #03335402001)] and 1 mM DTT [Sigma #43186]. An additional 9 ml of isolation buffer was added to wash the strainer. The final 15 ml of solution was mixed by inverting the tube 10x and carefully pipetted into two ultracentrifuge tubes (Beckman Coulter #344059) onto the isolation buffer cushion (5 ml) without disrupting the phases. The tubes were centrifuged at 30,000 x g for 60 min at 4ºC on an ultracentrifuge (Beckman L7-65) and rotor (Beckman SW41-Ti). Following the ultracentrifugation, the supernatant was carefully and completely removed, and 100 µl of resuspension buffer (250 mM sucrose [Sigma #S0389], 25 mM KCl [Sigma #60142], 5 mM MgCl2 [Sigma #M1028], 20 mM Tris-HCl [pH 7.5; AmericanBio #AB14043; Sigma #T2413], protease inhibitors without EDTA [Roche #11836170001], RNAse inhibitor [80 U/ml; Roche #03335402001], and 1 mM DTT [Sigma #43186]) was added dropwise on the pellet in each tube and incubated on ice for 15 min. Pellets were gently dissolved by pipetting 30x with a 1 ml pipette tip, pooled, and filtered through a 35-µm tube top cell strainer (Corning #352235). Finally, nuclei were counted on a Countess cell counter (ThermoFisher) and diluted to 1 million/ml with sample-run buffer (0.1% bovine serum albumin [Gemini Bio-Products #700-106P], RNAse inhibitor [80 U/ml; Roche #03335402001], and 1 mM DTT [Sigma #43186]) in Dulbecco's phosphate-buffered saline (Gibco #14190).
single nuclei multiome (snRNA-seq and snATAC-seq):
The nuclei samples were placed on ice and taken to the Yale Center for Genome Analysis core facility, where they were processed with targeted nuclei recovery of 20,000 nuclei per sample on a microfluidic Chromium System (10x Genomics) following the manufacturer’s protocol (10x Genomics, Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, PN-1000283). Libraries were sequenced with paired-end 150 bp reads on an Illumina NovaSeq 6000 to a target depth of 250 million read pairs per sample.

value: post mortem human brain

tag: age death_(yrs)

value: female

tag: pmi (hrs)

tag: diagnosis


title: RT00389N snATAC-seq


title: SK-MEL-147 cells, shSCR control, 6 days, replicate 3

description:
SCR-SRCAP-6d-rep1
YL1_SRCAP_P400_d6_normcounts.txt


title: lung_WT_ATR234.1


title: heart_WT_ATR234.2


title: SK-MEL-147 cells, YL1 knockdown sh84, 6 days, replicate 2

description:
shYL1_vs_SCR_d6.csv
shYL1-sh84-6d-rep2
YL1_SRCAP_P400_d6_normcounts.txt

value: YL1 knockdown


title: RT00388N snATAC-seq


title: heart_WT_ATR234.1


title: RT00387N snATAC-seq


title: lung_Mut_ATR237.2


title: RT00386N snATAC-seq


title: B6_BM-H3K27me3-m1-2_H5VTLBGXB_S14

city: Utrecht

first: Jake

last: Yeung

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
genomicDNA_cut_from_MNase-ProteinA_with_staining_of_H3K27me3
B6-13W1-BM-H3K27me3-4-merged.filtered.bincounts.slidewin.csv.gz

data_processing:
fastq files were mapped using BWA-0.7.16a (r1181) to ENSEMBL Build 95
Cells in the top 95% of UMI counts and fraction counts starting with "TA" are kept as "good cells".
Bins were created using 100 kb sliding window with step size of 20 kb.
Genome_build: mm10
Supplementary_files_format_and_content: Genomic bins to cells binned across genomic regions.

extract_protocol:
Femur and Tibia were extracted, the bones ends were cut away to access the bone marrow which was flushed out using a 22G syringe with HBSS (-ca, -mag, -phenol red, Gibco 14175053) supplemented with Pen-Strep and 1% FCS. The bone marrow was dissociated and debris was removed by passing it through a 70um cell strainer (Corning, 431751). Cells were washed with 25ml supplemented HBSS before depleting the sample of unnucleated cells using IOTest 3 Lysing solution (Beckman Coulter) following provider instructions. Cells were washed additional 2 times with PBS before processing them by the scChIC protocol for the 4 different histone modifications.
Cells were resuspended in 500ul wash buffer (47.5ml H2O RNAse free, 1ml 1M HEPES pH 7.5, 1.5ml 5M NaCl, 3.6ul pure spermidine solution). Aliquot in a 0.5ml protein low-binding tubes (1 per antibody to be used). Following steps are performed on ice.  Cells were pelleted at 600g for 3min and resuspended in 400 ul Wash Buffer 1 (wash buffer with extra 0.05% saponin (Sigma Aldrich), protease inhibitor cocktail (Sigma Aldrich), 4 ul/ml 0.5M EDTA) containing the primary antibody (1:100 dilution for H3K4me1, H3K9me3 and H3K27me3 and 1:200 dilution for H3K4me3, Saponin has to be prepared fresh every time as a 10% solution in PBS). Cells were incubated overnight at 4oC on a roller, before they were washed once with 500 ul Wash Buffer 2 (wash buffer with extra 0.05% saponin, protease inhibitor).  Afterwards cells were resuspended in 500 ul Wash Buffer 2 containing PaMN (3ng/ml) and incubated for 1h at 4C on a roller.  Finally, cells were washed an additional 2 times with 500 ul Wash Buffer 2 before passing it through a 70um cell strainer (Corning, 431751) and sorting them on a JAZZ FACS machine into 384 well plates containing 50nl Wash buffer 3 (Wash buffer containing 0,05% saponin) and 5ul sterile filtered mineral oil (Sigma Aldrich) per well. Small volumes were distributed using a Nanodrop II system (Innovadyme). 50nl of Wash Buffer 3, containing 4uM CaCl2, were added per cell to induce Protein A-MN mediated chromatin digestion that was performed for 30min on ice. Afterwards the reaction was stopped by adding 100nl of a stop solution containing 40mM EGTA (chelates Ca2+ and stops MN), 1.5% NP40 and 10ul 2mg/ml proteinase k (Ambion). Chromatin is subsequently released and PaMN permanently destroyed by proteinase k digestion at 65C for 6h followed by 80C for 20min to heat inactivate proteinase k. Afterwards plates can be stored at -20C until further processing.
DNA fragments are further blunt ended using Klenow large fragment (NEB) and T4 PNK (NEB) in the presence of dNTPs. Afterwards nonintegrated dNTPs are removed using schrimp alkaline phosphatase (NEB) to increase A-tail efficiency. Subsequently blunt fragments are A-Tailed using AmpliTaq™ 360 DNA Polymerase (Thermofisher) in the presence of fresh dATP and T4 PNK (NEB). Next fragments are ligated to T-tail adaptors containing 3 bp UMIs and an 8bp cell barcode (final concentration 9nM from IDT) for 16h at 16C using T4-ligase (NEB). Adaptors were added with a Mosquito HTS (ttp labtech). Ligation products were pooled by centrifugation and cleaned using Ampure XP beads at a bead to sample ratio of 0.8 (Beckman Coulter). The cleaned DNA is then linear amplified by invitro transcription with components of MessageAmp II (Invitrogen) for 16h at 37C. The produced RNA is purified 1-3 times depending on Adaptor dimer contamination using RNA Clean XP beads (Beckman Coulter) at 0.8 beads to sample ratio, followed by RNA fragmentation for 2.5 min at 94C. After another bead cleanup, 20% of the RNA is reverse transcribed with Superscript II (NEB) and PCR amplified to add the Illumina smallRNA barcodes and handles with NEBNext Ultra II Q5 Master Mix. PCR cycles depended on the abundance of the histone modification assayed and the number of RNA cleanup cycles after IVT needed (8-10 for H3K9me3 and H3K27me3 10-12 for H3K4me1 and 12-15 for H3K4me3).

value: bone marrow


title: RT00385N snATAC-seq

value: Control


title: B6_BM-H3K4me1-m1-4_H5VTLBGXB_S4

description:
genomicDNA_cut_from_MNase-ProteinA_with_staining_of_H3K4me1
B6-13W1-BM-H3K4me1-1-merged.filtered.bincounts.slidewin.csv.gz


title: SK-MEL-147 cells, YL1 knockdown sh30, 6 days, replicate 2

description:
shYL1_vs_SCR_d6.csv
shYL1-sh30-6d-rep2
YL1_SRCAP_P400_d6_normcounts.txt


title: B6_BM-H3K4me1-m1-1_H5VTLBGXB_S1


title: SK-MEL-147 cells, YL1 knockdown sh30, 6 days, replicate 1

description:
shYL1_vs_SCR_d6.csv
shYL1-sh30-6d-rep1
YL1_SRCAP_P400_d6_normcounts.txt


title: RT00384N snATAC-seq


title: SK-MEL-147 cells, shSCR control, 6 days, replicate 2

description:
SCR-YL1-6d-rep2
YL1_SRCAP_P400_d6_normcounts.txt


title: BM-H3K27me3-m2-1_AH3VGVBGX9_S6

description:
genomicDNA_cut_from_MNase-ProteinA_with_staining_of_H3K27me3
BM-H3K27me3-build95.txt.gz

source_name: BM

value: FVB


title: SK-MEL-147 cells, shSCR control, 6 days, replicate 1

description:
SCR-YL1-6d-rep1
YL1_SRCAP_P400_d6_normcounts.txt

value: Melanoma


title: RT00391N snATAC-seq


title: B6_BM-H3K9me3-m1-1_H5VTLBGXB_S9

description:
genomicDNA_cut_from_MNase-ProteinA_with_staining_of_H3K9me3
B6-13W1-BM-H3K9me3-4-merged.filtered.bincounts.slidewin.csv.gz


title: RT00381N snATAC-seq


title: SK-MEL-147 cells, YL1 knockdown sh84, 3 days, replicate 2

description:
shYL1_vs_SCR_d3.csv
shYL1-sh84-3d-rep2
YL1_d3_normcounts.txt


title: B6_BM-H3K4me3-m1-3_H5VTLBGXB_S7

description:
genomicDNA_cut_from_MNase-ProteinA_with_staining_of_H3K4me3
B6-13W1-BM-H3K4me3-1-merged.filtered.bincounts.slidewin.csv.gz


title: SK-MEL-147 cells, YL1 knockdown sh84, 3 days, replicate 1

description:
shYL1_vs_SCR_d3.csv
shYL1-sh84-3d-rep1
YL1_d3_normcounts.txt


title: SK-MEL-147 cells, YL1 knockdown sh84, 6 days, replicate 1

description:
shYL1_vs_SCR_d6.csv
shYL1-sh84-6d-rep1
YL1_SRCAP_P400_d6_normcounts.txt


title: RT00380N snATAC-seq


title: SK-MEL-147 cells, YL1 knockdown sh30, 3 days, replicate 2

description:
shYL1_vs_SCR_d3.csv
shYL1-sh30-3d-rep2
YL1_d3_normcounts.txt


title: B6_BM-H3K4me1-m1-3_AH5W5KBGXB_S3


title: SK-MEL-147 cells, YL1 knockdown sh30, 3 days, replicate 1

description:
shYL1_vs_SCR_d3.csv
shYL1-sh30-3d-rep1
YL1_d3_normcounts.txt


title: B6_BM-H3K9me3-m1-2_AH5WT3BGXB_S10


title: B6_BM-H3K9me3-m1-3_H5VTLBGXB_S11


title: B6_BM-H3K9me3-m1-3_AH5W5KBGXB_S11


title: RT00378N snATAC-seq


title: SK-MEL-147 cells, shSCR control, 3 days, replicate 2

description:
SCR-YL1-3d-rep2
YL1_d3_normcounts.txt


title: RT00379N snATAC-seq


title: RT00377N snATAC-seq


title: RT00376N snATAC-seq


title: MethylC-seq_Cnt-1_IBM1-ox-L3

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

data_processing:
Bisulfite-seq: Methylpy (Schultz et al., 2015) with Cutadapt v1.9 and Bowtie 2.2.4.
RNA-seq: Trimmomatic v0.33 for filtering reads and Kallisto v0.50.0 for mapping
Assembly: Tair10 for Arabidopsis thaliana
Assembly: RS08 for Raphanus raphanistrum (https://ngdc.cncb.ac.cn/gwh/Assembly/9805/show)
Assembly: ASM90040641v1 assembly for I. lusitanica (PRJEB26555 in EBI)
Supplementary files format and content: compressed tab-separated text files in allc format. "allc" stands for all cytosine (C). Each row in an allc file corresponds to one cytosine in the genome. An allc file contain 7 mandatory columns and no header (https://github.com/yupenghe/methylpy#output-format).
Supplementary files format and content: raw count files including target_id, length, eff_length, est_counts, and tpm for RNA-seq data.

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: Plants were grown at 23C under 15 hours of day light condition.

extract_protocol:
genomic DNA was isolated from leaf tissues using the DNeasy Plant Mini Kit (Qiagen), RNA was isolated from leaf tissues using the Qiagen Plant Mini Kit
MethylC-seq libraries were constructed using the MethylC-seq protocol (Urich et al., 2015). Briefly, genomic DNA was sonicated to around 200 bp using a Covaris S-series focused ultrasonicator, and end-repaired with an End-It DNA end-repair kit (Epicentre). The end-repaired DNA was subjected to A-tailing using Klenow 3′–5′ exo− (NEB) and ligated to methylated adapters using T4 DNA ligase (NEB). The ligated DNA was treated with sodium bisulfite reagent using the EZ DNA methylation-Gold kit and amplified using KAPA HiFi uracil + Readymix Polymerase. RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina) following the manufacturer’s instructions with limited modifications.

value: leaf


title: BM-H3K4me3-m1-1_AH3VGVBGX9_S10

description:
genomicDNA_cut_from_MNase-ProteinA_with_staining_of_H3K4me3
BM-H3K4me3-build95.txt.gz


title: SK-MEL-147 cells, shSCR control, 3 days, replicate 1

description:
SCR-YL1-3d-rep1
YL1_d3_normcounts.txt


title: RT00383N snATAC-seq


title: BM-H3K4me3-m2-1_H2GV2BGX9_S16


title: RT00375N snATAC-seq


title: BM-H3K27me3-m2-2_H2GV2BGX9_S18


title: RT00382N snATAC-seq


title: RT00374N snATAC-seq


title: MethylC-seq_Cnt-1_IBM1-ox-L2


title: BM-H3K4me1-m1-1_AH3VGVBGX9_S9

description:
genomicDNA_cut_from_MNase-ProteinA_with_staining_of_H3K4me1
BM-H3K4me1-build95.txt.gz


title: MethylC-seq_Cnt-1_IBM1-ox-L1


title: BM-H3K4me1-m2-2_H2GV2BGX9_S15


title: RT00373N snATAC-seq


title: MethylC-seq_Cnt-1_WT


title: B6_BM-H3K4me1-m1-3_AH5WT3BGXB_S3


title: B6_BM-H3K27me3-m1-4_AH5WT3BGXB_S16


title: B6_BM-H3K4me3-m1-4_AH5W5KBGXB_S8


title: FAKi day 21 Replicate 1

city: La Jolla

first: Kathryn

last: Lande

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute

data_processing:
(Alignment) Raw reads were trimmed with Trim Galore and quality-checked with FastQC v0.11.8. Trimmed reads were then aligned to the hg38 human reference genome with STAR aligner v2.5.3a, and converted to gene counts with the analyzeRepeats.pl script in HOMER.
Differential expression analysis was performed with DESeq2.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: 92.1 UM cells (RRID:CVCL_8607) were grown in RPMI media containing 10% FBS (Atlanta Biologicals) and 1% penicillin/streptomycin (Corning).

extract_protocol:
RNA was isolated using E.Z.N.A. Total RNA kit I (Omega)
mRNA sequencing libraries were prepared according to manufacturer’s protocol using RNA using Illumina TruSeq Stranded mRNA library preparation kit (Illumina).

treatment_protocol: 92.1 UM cells were treated with either 100nM of the FAKi VS-4718 or DMSO for a period of 21 days.  Treatments and media were refreshed every 72hr.

value: Uveal Melanoma

tag: day

value: FAKi


title: FAKi day 21 Replicate 3


title: FAKi day 21 Replicate 2


title: RT00391N snRNA-seq

value: male


title: DMSO day 21 Replicate 2

value: DMSO


title: B6_BM-H3K9me3-m1-4_AH5W5KBGXB_S12


title: BM-H3K9me3-m2-1_H2GV2BGX9_S17

description:
genomicDNA_cut_from_MNase-ProteinA_with_staining_of_H3K9me3
BM-H3K9me3-build95.txt.gz


title: DMSO day 21 Replicate 1


title: DMSO day 21 Replicate 3


title: RT00390N snRNA-seq


title: BM-H3K4me1-m2-1_AH3VGVBGX9_S3


title: B6_BM-H3K4me1-m1-1_AH5WT3BGXB_S1


title: FAKi day 14 Replicate 3


title: RT00389N snRNA-seq


title: RT00387N snRNA-seq


title: RT00386N snRNA-seq


title: FAKi day 14 Replicate 2


title: RT00385N snRNA-seq


title: B6_BM-H3K9me3-m1-1_AH5WT3BGXB_S9


title: RT00384N snRNA-seq


title: RT00372N snATAC-seq


title: B6_BM-H3K27me3-m1-2_AH5WT3BGXB_S14

description:
genomicDNA_cut_from_MNase-ProteinA_with_staining_of_H3K27me3
B6-13W1-BM-H3K27me3-4-merged.filtered.bincounts.slidewin.csv.gz


title: FAKi day 14 Replicate 1


title: DMSO day 14 Replicate 3


title: RT00383N snRNA-seq


title: B6_BM-H3K9me3-m1-3_AH5WT3BGXB_S11


title: RT00388N snRNA-seq


title: DMSO day 14 Replicate 2


title: DMSO day 14 Replicate 1


title: B6_BM-H3K27me3-m1-1_H5VTLBGXB_S13


title: SG-UPF3KD-3

city: Birmingham

first: Matthew

last: Wright

address: Edgbaston

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

data_processing:
Sequences trimmed using TRIMMOMATIC PE (v.39)
Sequences aligned to Dm6.56 using HISAT2 (v2.2.1)
SAMtools (v1.19.2) to sort and convert sam files to BAM files
HTSeq (v0.13.5) to calculate raw counts from bam files
DESeq2 for differential expression analysis
Assembly: Dm6.56 FlyBase (https://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6.56_FB2024_01/)
Supplementary files format and content: Raw gene counts in plain .txt files, annotated with FlyBase Gene ID

organism: Drosophila melanogaster

source_name: Salivary Glands

growth_protocol: Flies grown at 25 degrees celcius on standard cornmeal food

extract_protocol:
RNA was extracted using TRIzol. The upper phase was taken, and RNA was precipitated. Precpitated RNA was dissolved in dH2O. 1 µg of RNA was used for library construction and sequencing.
Poly(A) RNA was enriched from total RNA using NEBNext Poly(A) Magnetic Isolation Module (New England Biolabs E7490L). Libraries constructed using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolab E7420L), and NEBnext Multiplex Oligos for Illumina Dual Index Primers.

value: Salivary Glands

value: w; UAS-UPF3RNAi/+; FkhGAL4


title: RT00381N snRNA-seq


title: B6_BM-H3K4me1-m1-4_AH5W5KBGXB_S4

description:
genomicDNA_cut_from_MNase-ProteinA_with_staining_of_H3K4me1
B6-13W1-BM-H3K4me1-1-merged.filtered.bincounts.slidewin.csv.gz


title: SG-UPF3KD-2


title: FAKi day 7 Replicate 3


title: RT00380N snRNA-seq


title: B6_BM-H3K27me3-m1-4_H5VTLBGXB_S16


title: RT00379N snRNA-seq


title: SG-UPF3KD-1


title: DMSO day 7 Replicate 3


title: RT00378N snRNA-seq


title: BM-H3K9me3-m1-2_AH3VGVBGX9_S1


title: RT00377N snRNA-seq


title: B6_BM-H3K9me3-m1-4_H5VTLBGXB_S12


title: B6_BM-H3K4me3-m1-1_AH5W5KBGXB_S5


title: FAKi day 7 Replicate 1


title: SG-UPF2KD-3

value: w; +; FkhGAL4/UAS-UPF2RNAi


title: DMSO day 7 Replicate 2


title: BM-H3K9me3-m1-1_H2GV2BGX9_S13


title: RT00376N snRNA-seq


title: SG-UPF2KD-2


title: RT00382N snRNA-seq


title: SG-UPF2KD-1


title: DMSO day 7 Replicate 1


title: SG-UPF1KD-3

value: w; UAS-UPF1RNAi/+; FkhGAL4


title: BM-H3K4me3-m1-2_H2GV2BGX9_S12


title: FAKi day 3 Replicate 3


title: RT00374N snRNA-seq


title: B6_BM-H3K4me1-m1-3_H5VTLBGXB_S3


title: FAKi day 7 Replicate 2


title: RT00373N snRNA-seq


title: FAKi day 3 Replicate 2


title: BM-H3K9me3-m2-2_AH3VGVBGX9_S5


title: SG-UPF1KD-1


title: B6_BM-H3K4me1-m1-2_AH5W5KBGXB_S2


title: DMSO day 3 Replicate 3


title: SG-WT-3

value: w; +; FkhGAL4/+


title: SG-WT-2


title: FAKi day 3 Replicate 1


title: DMSO day 3 Replicate 2


title: SG-WT-1


title: DMSO day 3 Replicate 1


title: B6_BM-H3K9me3-m1-2_AH5W5KBGXB_S10


title: RT00375N snRNA-seq

value: post mortem human brain


title: B6_BM-H3K4me3-m1-1_H5VTLBGXB_S5


title: neonatal ventricular cardiac fibroblasts, si-Foxm1_3

city: Shanghai

first: shuai

last: song

address: No. 1609 Xietu Road, Xuhui District, Shanghai

department: Department of Cardiology

country: China

institute: Zhongshan  Hospital, Fudan University

data_processing:
fastp software was used to process raw reads in fastq format. clean reads were obtained after low-quality reads were removed for subsequent data analysis.
Clean reads were compared with mm39 reference genome using HISAT2 software, and gene expression volume (FPKM) was calculated. The reads of each gene were obtained by HTSeq-count.
Assembly: mm39
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit(Ambion) followingthe manufacturer's protocol. 4 μg of total RNA was used to construct sequencing libraries.
RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number(RIN)≥ 7 were subjected to the subsequent analysis. The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (llumina, San Diego, CA, USA) according to the manufacturer's instructions. Then these libraries were sequenced on the llumina sequencing platform.

tag: group


title: Beas-2B cells, siFOXK2_2 1

city: Columbus

first: Rama

middle: K

last: Mallampalli

state: Ohio

address: 473 W12th Avenue.

department: Department of Internal Medicine

institute: The Ohio State University

data_processing:
We conducted essential quality control procedures on the raw sequencing data using FastQC v0.12 (PMID: 21278150) and MultiQC v1.16 (PMID: 27312411).
read trimming was performed with TrimGalore v0.6.10 (PMID: 27474005) using default parameters.
The resulting reads were aligned to the GRCh38 reference genome, and read quantification was carried in both alignment steps utilizing STAR v2.7.11a (PMID: 23104886) with its default settings.
To generate the combined counts matrix, we imported and merged each STAR output file using base R functions in conjunction with the tidyverse package v2.0.0. This matrix was then converted into a DESeq2 object using the DESeqDataSetFromMatrix() function, with the groups siFOXK2 and siCON designated for contrast.
Data normalization and differential expression analysis were conducted using the DESeq2 package v3.17 (PMID: 25516281).
Assembly: GRCh38 reference genome
Supplementary files format and content: tab-delinited text file includes raw counts for each sample
Supplementary files format and content: tab-delinited text file includes RPKM counts for each sample

extract_protocol:
Total RNA was isolated from cells using the RNeasy Plus Kit (Qiagen) according to the manufacturer's instructions.
total RNA was isolated from cells using the RNeasy Plus Kit (Qiagen) according to the manufacturer's instructions.

value: Lung epithelial cells

value: FoxK2 knockdown


title: Beas-2B cells, siFOXK2_1 3


title: DMSO day 0 Replicate 3


title: SG-UPF1KD-2


title: neonatal ventricular cardiac fibroblasts, si-Foxm1_2


title: Beas-2B cells, siFOXK2_1 2


title: DMSO day 0 Replicate 2


title: neonatal ventricular cardiac fibroblasts, si-Foxm1_1


title: RT00372N snRNA-seq


title: B6_BM-H3K27me3-m1-2_AH5W5KBGXB_S14

value: bone marrow


title: Beas-2B cells, siFOXK2_2 3


title: Beas-2B cells, siFOXK2_1 1


title: DMSO day 0 Replicate 1


title: Beas-2B cells, siFOXK2_2 2


title: B6_BM-H3K27me3-m1-3_H5VTLBGXB_S15


title: Nanocapsule treated, replicate 1, scRNAseq

description: 10x Genomics

value: Cancer cells

value: Tumor

value: 6-8 weeks old

value: Nanocapsule


title: Beas-2B cells, siRNA Scrambled 3

value: WT


title: MT9 CYSLTR2 L129Q replicate 3

growth_protocol: HEK 293T cells were grown in DMEM supplemented with fetal bovine serum (FBS) (10%), penicillin (100 U/ml) and streptomycin (100 μg/ml).

extract_protocol:
RNA was isolated using miRNeasy Kit (QIAGEN)
mRNA sequencing libraries were prepared according to manufacturer’s protocol using RNA using Illumina TruSeq Stranded mRNA library preparation kit (Illumina).

treatment_protocol: HEK 293T cells were plated in a 6-well plate in DMEM supplemented with 10% FBS, penicillin (100 U/ml) and streptomycin (100 μg/ml) 24 hours before transfection. The following day, cells were transfected with expression plasmids with duplex containing 0.25 μg of DNA, 250 μl of optimem and 10 μl of Lipofectamine 2000 per well.

value: kidney epithelial, embryonic

value: CYSLTR2 L129Q


title: Beas-2B cells, siRNA Scrambled 2


title: B6_BM-H3K27me3-m1-3_AH5W5KBGXB_S15


title: B6_BM-H3K4me1-m1-1_AH5W5KBGXB_S1


title: neonatal ventricular cardiac fibroblasts, OE-Foxm1_3


title: neonatal ventricular cardiac fibroblasts, OE-NC_1

value: OE-NC


title: MT8 GNAQ Q209L replicate 3

value: GNAQ Q209L


title: MT7 WT replicate 3


title: Beas-2B cells, siRNA Scrambled 1


title: B6_BM-H3K4me3-m1-4_H5VTLBGXB_S8


title: B6_BM-H3K9me3-m1-1_AH5W5KBGXB_S9


title: Mdivi1_MCseq_Treatment

city: seoul

first: Jueng Soo

last: You

address: 120 Neungdong-ro

country: South Korea

institute: Konkuk University

data_processing:
After sequencing, the raw sequence reads are filtered based on quality. The adapter sequences are also trimmed off the raw sequence reads.
The trimmed reads are mapped to reference genome with BSMAP which is based on the SOAP (Short Oligo Alignment Program).
The only uniquely mapped reads are selected to sort, index and PCR duplicates are removed with SAMBAMBA (v0.5.9).
The methylation ratio of every single cytosine location within on-target region is extracted from the mapping results using 'methylatio.py' script in BSMAP. The results of the coverage profiles were calculated as # of C /effective CT counts for each cytosine in CpG, CHH and CHG.
Each cytosine locus in CpG, CHH and CHG is annotated using table browser function of UCSC genome browser. Annotation includes functional location of each gene (promoter regions which are defined as -2kb upstream of the transcription start site, exons and introns etc.), transcripts ID, gene ID, strand and CpG island.
Assembly: hg19
Supplementary files format and content: Methylation ratio of single cytosine locations are in the txt file.

extract_protocol:
Genomic DNA was isolated from control or Mdivi-1 treated SH-SY5Y cells by use of Wizard® Genomic DNA Purification Kit(Promega, Madison, WI, United States).
RNA-Seq library construction was performed using SureSelectXT Methyl-Seq Reagent Kit(Agilent, Santa Clara, CA, United States) and sequenced using NovaSeq 6000 Sequencing System (Illumina, San Diego, CA, United States).
Methyl capture sequncing


title: B6_BM-H3K9me3-m1-2_H5VTLBGXB_S10


title: neonatal ventricular cardiac fibroblasts, OE-Foxm1_2


title: Mdivi1_MCseq_Control

value: DMSO


title: B6_BM-H3K27me3-m1-4_AH5W5KBGXB_S16


title: neonatal ventricular cardiac fibroblasts, OE-Foxm1_1


title: neonatal ventricular cardiac fibroblasts, OE-NC_3


title: neonatal ventricular cardiac fibroblasts, OE-NC_2


title: neonatal ventricular cardiac fibroblasts, si-NC_3

value: si-NC


title: B6_BM-H3K4me1-m1-2_AH5WT3BGXB_S2


title: MT3 CYSLTR2 L129Q replicate 1


title: neonatal ventricular cardiac fibroblasts, si-NC_2


title: MT4 WT replicate 2


title: BE2-shMETTL14-2-IP

city: Suzhou

first: Jianwei

last: Wang

address: No.92 Zhongnan street

institute: Children's hospital of scoochow university

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster.
After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-clusters.
After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Total RNAs were extracted from neuroblastoma cells using TRIzol Reagent (Invitrogen, cat. NO 15596026）following the methods by Chomczynski et al. DNA digestion was carried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with NanodropTM OneCspectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies, Q10210)
50 μg total RNAs were used for polyadenylated RNA enrichment by VAHTS mRNA Capture Beads. 20mM ZnCl2 was added to mRNA and incubated at 95℃ for 5min-10min until the RNA fragments were mainly distributed in 100-200 nt. Then 10% RNA fragments was saved as Input and the rest was used for m6A immunoprecipitation（IP）.The specific anti-m6A antibody (Synaptic Systems, 202203) was applied for m6A immunoprecipitation. RNA samples of both input and IP were prepared using TRIzol reagent. The stranded RNA sequencing library was constructed by KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina(Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer's instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on DNBSEQ-T7 sequencer (MGI Tech Co., Ltd. China) with PE150 model.

value: Neuroblastoma cells


title: BE2-shMETTL14-1-input


title: B6_BM-H3K9me3-m1-4_AH5WT3BGXB_S12


title: neonatal ventricular cardiac fibroblasts, si-NC_1


title: MT2 GNAQ Q209L replicate 1


title: BE2-shMETTL14-1-IP


title: B6_BM-H3K4me3-m1-3_AH5WT3BGXB_S7


title: neonatal ventricular cardiac fibroblasts, si-Foxm1+Ang-II_3


title: B6_BM-H3K27me3-m1-1_AH5W5KBGXB_S13


title: mouse_PTGR_unsorted_rep1

description:
mouse_PTGR_unsorted_rep1_counts_same_strand.txt
mouse_PTGR_unsorted_rep1_counts_rev_strand.txt
mouse_PTGR_screen_sorted_vs_unsorted.txt

data_processing:
First, iPCR reads from sorted and background (non-selected) samples were trimmed using Trim galore (v0.6.0) with default parameters to remove Illumina adapters. Then, trimmed reads were aligned to the mm10 version of the mouse genome (mouse assays) or to the hg38 version of the human genome (human assays) using bowtie216 with default parameters (for paired-end sequenced samples, only first mate reads were considered), before removal of duplicated and low mapping quality reads (mapq<=30) using samtools (v1.9)17. Mapped insertions were assigned to the closest downstream exon junction – with a maximum distance of 200kb – based on GENCODE annotations of the mouse genome (vM25, mouse assays) or of the human genome (v43, human assays). Finally, insertion counts were aggregated per gene. Of note, only exons from protein-coding transcripts were considered, except for the first exon of each transcript, which might not contain splicing acceptor sites. Consequently, intronless genes – for which none of the isoforms contain a spliced intron – were not considered.
For each species, background replicates showed reproducible gene counts and therefore were merged, and genes with at least one insertion were considered as putatively tagged. Finally, genes showing significantly more insertions in sorted samples compared to merged background samples were identified using one-tailed fisher's exact test (alternative= "greater") on merged biological replicates. Of note, only genes with at least 3 unique insertions in sorted samples were considered. Obtained p-values were corrected for multiple testing using the FDR method and genes showing an FDR<0.001 and a log2 Odd Ratio≥1 were classified as hits.
Assembly: mm10 (mouse) and hg38 (human)
Supplementary files format and content: counts_same_strand files contains the genomic coordinates of all the insertion that were found in the sample, and the id of the assigned gene. In addition, the distance between the insertion and the exon that was used for assignment, as well as its position (number) inside the gene, are reported.
Supplementary files format and content: counts_rev_strand is similar to the previous (counts_same_strand) file, but report the assignment of reversed insetions. Used to compute strand bias.
Supplementary files format and content: The sorted_vs_unsorted.txt files contain, for each gene, the unique insertions enrichment in sorted vs unsorted samples (log2OR) with the associated FDR (padj). In this study, all genes with a FDR<0.001 were considered as hits (see "hit" column).
Library strategy: ORFtag

growth_protocol: All mouse experiments presented here were carried out in diploid mouse embryonic stem cells (mESCs) that were derived from originally haploid HMSc2 termed AN3-128. The mESCs were cultivated without feeders in high-glucose-DMEM (Sigma-Aldrich) supplemented with 13.5% fetal bovine serum (Sigma-Aldrich), 2 mM L-glutamine (Sigma-Aldrich), 1x Penicillin-Streptomycin (Sigma-Aldrich), 1x MEM non-essential amino acid solution (Gibco), 1mM sodium pyruvate (Sigma-Aldrich), 50 mM β-mercaptoethanol (Merck) and in-house produced recombinant LIF. Human ORFtag experiments were carried out in RKO (activator screen, ATCC, CRL-2577) or HEK293 (repressor screen, ATCC, CRL-1573) and the cells were cultivated in high-glucose-DMEM (Sigma-Aldrich) supplemented with 10% fetal bovine serum (Sigma-Aldrich), 2 mM L-glutamine (Sigma-Aldrich), 1x Penicillin-Streptomycin (Sigma-Aldrich). Virus packaging cell lines, Lenti-X 293T (Takara), PlatinumE (Cell Biolabs) and PlatinumA (Cell Biolabs), were grown according to the manufacturer’s instructions. All cell lines were cultured at 37°C and 5% CO2 and regularly tested for mycoplasma contamination.

extract_protocol:
Genomic locations of ORFtag integrations were mapped using modified inverse-PCR followed by next generation sequencing (iPCR-NGS) protocol8. Genomic DNA was prepared by lysing cell pellets in lysis buffer (10 mM Tris-HCl pH 8.0, 5 mM EDTA, 100 mM NaCl, 1% SDS, 0.5 mg/ml proteinase K) at 55°C overnight. Following a 2-hour RNase A treatment (Qiagen, 100 mg/ml, 1:1,000 dilution) at 37°C, two extractions using phenol:chloroform:isoamyl alcohol and one extraction using chloroform:isoamyl alcohol were carried out.
The samples then underwent two separate digestion reactions (with up to 4 µg of genomic DNA) using NlaIII and MseI enzymes (NEB) at 37°C overnight, followed by purification using a Monarch PCR&DNA Cleanup Kit (NEB). Ring-ligation was carried out using T4 DNA ligase (NEB) at 16 °C overnight, followed by heat-inactivation (65°C, 15 min) and linearization using SbfI-HF (NEB) at 37°C for 2 h. The digests were then purified using a Monarch PCR&DNA Cleanup Kit (NEB) and amplified using firstly a nested PCR reaction with KAPA HiFi HotStart ReadyMix (Roche), and a specific primer pair (TGCAGGACCGGACGTGACTGGAGTTC*A, TGCAGGACGATGAGCAGAGCCAGAACC*A) for 16 cycles. After cleanup with AMPure XP Reagent (Beckman Coulter, 1:1 ratio beads:PCR), iPCR amplification was carried out with KAPA HiFi HotStart ReadyMix (Roche), and a specific primer pair (AATGATACGGCGACCACCGAGATCTACACGAGCCAGAACCAGAAGGAACTTGA*C, CAAGCAGAAGACGGCATACGAGAT [custom-barcode] GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT) for 18 cycles. Afterwards, amplified libraries were size selected for a range of 400-800 bp using SPRIselect beads (Beckman Coulter). NGS was performed on an Illumina NextSeq550 or llumina HiSeq 2500 sequencer according to the manufacturers’ protocols with custom first-read primer (1:1 mix of GAGTGATTGACTACCCGTCAGCGGGGGTCTTTCA and TGAGTGATTGACTACCCACGACGGGGGTCTTTCA).

treatment_protocol: The ORFtag viral constructs were derived from the ecotropic Retro-EGT construct8 that includes the sequence features necessary for the inverse-PCR protocol (see below). Furthermore, the construct contains constitutively active PGK promoter that drives the expression of a NeoR resistance gene separated from a tag by the IRES sequence. The tag contained either TetR with an N-terminally located nuclear localization signal (Activator and Repressor screens; Addgene, this study) or LambdaN domain (PTGR screen; Addgene, this study). Additionally, the tag contained 2x GGGS-linker followed by the BC2-tag and 3xFLAG-tag. Finally, the ORFtag construct contains a consensus splice donor motif followed by a part of the Hprt intron (chrX:53020400-53020556 +, mm10). In order to tag genes in all three possible coding frames, three constructs were used that contain either 0, 1 or 2 additional nucleotides upstream of the consensus splice motif. Retroviral constructs carrying ORFtag cassette were packed in PlatinumE cell lines (for the screens performed in mESCs) or PlatinumA cell lines (for the screen performed in HEK293 cells) using polyethylenimine (PEI) reagent as described previously8. Reporter cell lines (100-150 million cells) were transduced with packaged retrovirus in the presence of 6 µg/ml polybrene (Sigma) and at low transduction efficiency (< 20%) to ensure only one virus per cells. Cells were harvested 24 hours later and plated in medium containing 0.1 mg/ml G418 (Gibco) for selection of transduced cells. Selection was continued until all cells on the control plate died (4-5 days), after which 40 million cells were processed as non-selected background for mapping of genomic integrations (see below). The remaining cells were sorted for GFP-positive (mouse and human Activator screens) or GFP-negative (mouse and human Repressor screens) populations using BD FACSAria III or IIu cell sorters (BD Biosciences) and processed for mapping of genomic integrations (see below). For the PTGR screen a five-sort strategy was applied to enrich cells that show a tethering dependent repression of reporter gene expression. Cells with a GFP expression equal to the lowest 10 percent of GFP expression observed after selection were sorted using BD FACSAria III and expanded thereafter. Additionally, non-sorted cells were maintained for gating of the consecutive sorts. Two additional sorts for cells with GFP expression similar to the lowest 10% of GFP signal observed in the non-sorted cells were performed and again expanded in-between the sorts. A fourth sort was performed for cells with a GFP expression equal to the lowest 5% of GFP signal observed in the non-sorted cells. After expansion, the cells were treated with 500nM 4-Hydroxytamoxifen (Sigma) to induce Cre-mediated recombination and to flox the boxB sites of the reporter construct and hence to revert the tethering. Thereafter a final sort was performed to select a cell population with a GFP expression equal to the highest 70% of GFP expressing cells. Transduction efficiency was measured by plating 10,000 cells on a 15-cm dish and selecting with G418 (Gibco). A control plate with 1,000 cells was also plated without selection. After 10 days, colonies were counted and transduction efficiency was calculated as the number of colonies on the selected plate divided by the total number of cells plated (10 times the number of colonies on the control plate).

value: mESC

value: wild-type cells with Puro-IRES-GFP-10xBoxB reporter randomly integrated, clonal cell line

value: unsorted


title: B6_BM-H3K4me3-m1-3_AH5W5KBGXB_S7


title: MT5 GNAQ Q209L replicate 2


title: MT1 WT replicate 1


title: BE2-shNC-2-input


title: MT6 CYSLTR2 L129Q replicate 2


title: BE2-shNC-1-input


title: mouse_PTGR_sorted_rep1

description:
mouse_PTGR_sorted_rep1_counts_same_strand.txt
mouse_PTGR_sorted_rep1_counts_rev_strand.txt
mouse_PTGR_screen_sorted_vs_unsorted.txt

value: sorted


title: BE2-shMETTL14-2-input


title: neonatal ventricular cardiac fibroblasts, si-Foxm1+Ang-II_1


title: B6_BM-H3K4me3-m1-2_AH5WT3BGXB_S6

value: bone marrow


title: BE2-shNC-2-IP


title: PYMT cells, BMP4-TGFB2_3

city: Bronx

first: Julio

middle: A

last: Aguirre-Ghiso

address: 1301 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

data_processing:
Raw sequence data (.bcl files) generated from the Illumina instrument was converted into fastq files and de- multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
The mouse genome reference used was GRCm38.p6 and GENCODE release M25 was used as the transcriptome reference. The alignment is performed by using STAR aligner (v2.7.5b)41. Gene level read counts are obtained by using Salmon (v1.2.1) for all libraries. All samples have passed the quality control requirements with > 85% of reads uniquely mapping (>25M uniquely mapped reads for each library) using STAR aligner.
Assembly: The mouse genome reference used was GRCm38.p6 and GENCODE release M25 was used as the transcriptome reference.
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PYMT

growth_protocol: PYMT cells were treated with 5ng/mL of TGFΒ2, BMP4, or both for 3 days, then media was changed, and cells were collected 2 days later (day3+2) after matrigel depolymerization (Corning, CLS354253) following the manufacturer’s instructions. 3 biological replicates were performed, and then RNA extraction, sample QC, library preparations, and sequencing reactions were conducted at GENEWIZ

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Plus Universal kit following the manufacturer’s instructions (Qiagen). Extracted RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies), and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies).
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following the manufacturer’s instructions (NEB). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First- strand and second-strand cDNAs were subsequently synthesized. cDNA fragments were end-repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR.
The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies), and quantified by using Qubit 2.0 Fluorometer (Invitrogen) as well as by quantitative PCR (KAPA Biosystems). The sequencing libraries were clustered on a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq instrument (4000 or equivalent) according to the manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired-End (PE) configuration. Image analysis and base calling were conducted by Illumina Control Software.

value: PYMT


title: neonatal ventricular cardiac fibroblasts, Ang-II_3

value: Ang-II


title: BM-H3K27me3-m1-1_H2GV2BGX9_S14

value: FVB


title: PYMT cells, BMP4-TGFB2_2


title: BE2-shNC-1-IP


title: neonatal ventricular cardiac fibroblasts, Ang-II_2


title: BM-H3K4me3-m2-2_AH3VGVBGX9_S4


title: B6_BM-H3K27me3-m1-1_AH5WT3BGXB_S13


title: neonatal ventricular cardiac fibroblasts, Ang-II_1


title: PYMT cells, BMP4-TGFB2_1


title: BM-H3K4me1-m1-2_H2GV2BGX9_S11


title: B6_BM-H3K4me1-m1-2_H5VTLBGXB_S2


title: neonatal ventricular cardiac fibroblasts, si-Foxm1+Ang-II_2


title: sample4_HT-29 shOGT

city: 浙江省

first: Huijuan

address: Yuhangtang Road No.866

institute: 浙大

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: colorectum

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: colorectum

value: Anchorrage-dependent cells

value: OGT knock down

value: colorectal tumor growth


title: PYMT cells, BMP4_3


title: PYMT cells, BMP4_2


title: sample3_HT-29 shScramble

value: WT


title: B6_BM-H3K27me3-m1-3_AH5WT3BGXB_S15


title: PYMT cells, BMP4_1


title: PYMT cells, TGFB2_3


title: sample2_HT-29 shScramble


title: B6_BM-H3K4me1-m1-4_AH5WT3BGXB_S4


title: B6_BM-H3K4me3-m1-2_AH5W5KBGXB_S6


title: PYMT cells, TGFB2_2


title: sample6_HT-29 shOGT


title: B6_BM-H3K4me3-m1-4_AH5WT3BGXB_S8


title: sample5_HT-29 shOGT


title: sample1_HT-29 shScramble


title: BM-H3K27me3-m1-2_AH3VGVBGX9_S2


title: THP-1_DMSO_rep1

city: shanghai

first: hezhou

last: guo

address: Shanghai, P. R. China.  No. 197 Rui Jin Er Road

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.8
Adapters and low-quality read ends were removed using Trimmomatic, based on quality control statistics generated by FastQC.
Quality filtered reads were then mapped to GRCh38 using Hisat2
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) . StringTie was used to quantify gene and isoform abundances.
R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R) was utilized for differential expression analysis.
Assembly: GRCh38
Supplementary files format and content: gene expression text file includes raw counts and FPKM values for each Sample

growth_protocol: THP-1 cells were grown in RPMI 1640 supplemented with 10% FBS, at 37 °C in a humidified atmosphere with 5% CO2

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 1 uM Decitabine or DMSO was incubated with THP-1 cells for 48 hours

value: human acute myeloid leukemia cells

value: THP-1 cells treated with DMSO


title: PYMT cells, TGFB2_1


title: PYMT cells, NT_3

value: NT


title: B6_BM-H3K4me3-m1-1_AH5WT3BGXB_S5


title: THP-1_Decitabine_rep2

value: THP-1 cells treated with Decitabine


title: PYMT cells, NT_2


title: B6_BM-H3K4me3-m1-2_H5VTLBGXB_S6


title: THP-1_Decitabine_rep1


title: PYMT cells, NT_1


title: pbmc18mEG2

status: Public on May 09 2024

first: Hailiang

last: Liu

address: NO 1239, siping road

institute: Tongji university

data_processing:
Illumina Casava1.7 software used for basecalling.
The resulting clean reads were saved in FASTQ format and subsequently aligned to the reference genome using HISAT2. The clean reads were aligned against the reference coding gene set using Bowtie2
Genes expression level is quantified through RSEM.
Differential expression analysis was carried out utilizing DESeq2, which identified genes with statistically significant differences at a threshold of Q < 0.05.
Assembly: GRCm38.84
Supplementary files format and content: FPKM ( Fragments Per Kilobase Million) for each Sample

source_name: peripheral blood mononuclear cells

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: Mice in the CRD group had their day and night phases inverted every 3 days in the first stage of the study for 4 weeks. In the second stage, the mice experienced 48 hours of light and 48 hours of dark alternately for 3 weeks. In the last stage, continuous light was provided for 1 week, during which irradiated food and sterile water were freely available.

value: peripheral blood mononuclear cells


title: pbmc18mEG1


title: tumor 3

city: Gainesville

first: Lizi

last: Wu

state: FL

address: 2033 Mowry Road

institute: University of Florida

description: LncRNA/mRNSexpression data

hyb_protocol: The labeled cRNAs were hybridized onto the Mouse LncRNA Array v3.0 (8 x 60K, Arraystar).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner G2505C using one color scan setting.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 4 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

source_name: tumor 3 for a third mouse

label_protocol: Sample labeling was performed based on the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar).

extract_protocol: Tissues or tumors were processed for RNA isolation after snap freezing in liquid nitrogen. Total RNA was extracted using Trizol reagent (Invitrogen) and purified by RNAeasy Mini Column (QIAGEN) NucleoSpin RNA Column.

value: tumor


title: pbmc18mCK2

treatment_protocol: Mice in the CON group were subjected to a 12-hour light (8:00–20:00)/dark (20:00–8:00) cycle, with free access to irradiated food and sterile water.


title: pbmc18mCK1


title: Normal control 2

description: LncRNA/mRNSexpression data

source_name: salivary gland tissue from normal control littermate (for the mouse with tumor 2)

value: Normal


title: Adjacent Normal 1

description: LncRNA/mRNSexpression data

source_name: Tumor 1-adjacent salivary gland tissue

value: Adjacent Normal


title: Tumor 2

description: LncRNA/mRNSexpression data

source_name: Tumor 2-adjacent salivary gland tissue

value: Tumor


title: Hyp_8wEGM4

source_name: hypothalamus

value: hypothalamus


title: THP-1_DMSO_rep2


title: Normal control  1

description: LncRNA/mRNSexpression data

source_name: salivary gland tissue from normal control littermate (for the mouse with tumor 1)


title: Adjacent Normal 2

description: LncRNA/mRNSexpression data


title: Tumor 1

description: LncRNA/mRNSexpression data

source_name: Tumor 1


title: tumor 4

description: LncRNA/mRNSexpression data

source_name: tumor 4 for a fourth mouse


title: Hyp_8wEGM3


title: Hyp_8wEGM2


title: Hyp_8wEGM1


title: Hyp_8wCKM5


title: Hyp_8wCKM1


title: Hyp_8wCKM2


title: Hyp_8wCKM3


title: Hyp_18mEG4


title: Hyp_18mEG3


title: Hyp_18mEG5


title: Hyp_8wCKM4


title: Hyp_18mEG1


title: Hyp_18mEG2


title: Hyp_18mCK4


title: Hyp_18mCK2


title: Hyp_8wEGM5


title: Hyp_18mCK1


title: Hip_8wEGM5

source_name: hippocampus

value: hippocampus


title: Hip_8wEGM3


title: Hip_8wEGM4


title: Hip_8wCKM4


title: Hip_8wEGM2


title: Hip_8wEGM1


title: Hip_8wCKM5


title: Hip_8wCKM3


title: Hip_8wCKM1


title: Hip_8wCKM2


title: Hip_18mEG3


title: Hip_18mEG4


title: Hip_18mEG2


title: Hip_18mEG5


title: Hip_18mEG1


title: Hip_18mCK2


title: Hip_18mCK1


title: Hip_18mCK3


title: Col_8wEGM3

source_name: colon

value: colon


title: Col_8wEGM4


title: Hyp_18mCK3


title: Col_8wEGM5


title: Hip_18mCK4


title: Col_8wCKM5


title: Col_8wCKM4


title: Col_8wCKM3


title: Col_8wEGM1


title: Col_8wEGM2


title: Col_8wCKM2


title: Col_18mEG5


title: Col_18mEG4


title: Col_18mEG3


title: Col_18mEG1


title: Col_18mCK4


title: Col_18mCK2


title: Col_18mCK3


title: Cec_8wEGM4

source_name: cecum

value: cecum


title: Col_18mCK1


title: Col_18mCK5


title: Cec_8wEGM5


title: Cec_8wEGM3


title: Cec_8wCKM4


title: Cec_8wCKM3


title: Cec_8wEGM1


title: Cec_8wEGM2


title: Cec_18mEG5


title: Cec_8wCKM2


title: Cec_8wCKM1


title: Cec_18mEG1


title: Cec_18mCK2


title: Cec_18mCK3


title: Cec_18mCK1


title: Cec_18mEG3


title: AH2Tg-3

city: Atlanta

first: Bingzhong

last: Xue

address: 50 Decatur St. SE

department: Biology

institute: Georgia State University

data_processing:
Primary sequencing data was produced by Illumina HiSeqTM 3000, the original image data is transferred into sequence data via base calling (Illumina GA Pipeline v1.5), which is defined as raw data or raw reads and saved as FASTQ file.
The ATACseq analysis was performed on the Galaxy server. Adaptor and quality trimming was performed using Trim Glore! Modules (Galaxy v0.4.3.1).
Trimmed reads were mapped to mouse genome mm10 using Bowtie2 (Galaxy v2.3.4.3) using default settings.
Reads mapped to the mitochondria genome were removed using Filter SAM or BAM function under the samtools module (Galaxy v1.8), and PCR duplicates were removed using MarkDuplicates from Picard tool v2.20.2. The mapped reads overlapping with ENCODE blacklist regions (version 2) were filtered before calling peaks.
ATACseq peak calling was performed using MACS2 v2.1.2 with the following command “-p 0.01 --nomodel --shift --100 --extsize 200 -B --SPMR --keep-dup all --call -summits”. BigWig files were generated by bedGraphtoBigwig and visualized in the Integrated genome viewer (IGV) v2.5.2.DiffBind (Galaxy v. 2.6.6.4) was used to identify differential peaks with a fixed window length of 400bp (summit ± 200bp)
Assembly: mm10
Supplementary files format and content: BigWig files of each sample  for peak visualization was provided.

source_name: subcutaneous white fat

extract_protocol:
Subcutaneoues white fat pad were removed, flash frozen in liquid nitrogen, tissues were dounce-homogenized, filtered, and centrifuged in iodixanol solution to obtain nuclei.
The nuclei were treated with Nextera Tn5 transposase (Illumina, San Diego, CA) for the transposition reaction, followed by DNA purification and PCR amplification with NEBNext 2X MasterMix (New England BioLabs, Ipswich, MA) and Nextera Index primers (Illumina).

value: subcutaneous white fat

value: 7 day cold exposure at 6 C


title: AH2Tg-2


title: Preinjection_Control_00dpi

city: West Haven

first: Sidi

last: Chen

state: CT

address: 850 West Campus Drive

institute: Yale University

data_processing:
Single-cell RNA-seq data were pre-processed with Cell Ranger v6.0.1 (10x Genomics) pipeline, using a standard pipeline that aligned reads to the mm10 mouse reference transcriptome and aggregated multiple datasets with the “agg” function.
Assembly: mm10 mouse reference from 10X Genomics website
Supplementary files format and content: Standard output files from Cell Ranger (matrix.mtx, barcodes.tsv, and features.tsv)

source_name: tissue culutre

extract_protocol:
The mRNA of AAVS1-KO and CALHM2-KO primary NK cells with or with cancer stimulations were extracted with RNeasy plus kit (Qiagen) according to manufacturer’s instruction.
NK cells were normalized to 1,000 cells / μL. Standard volumes of cell suspension were used for 10X Genomics gene expression library preparation to achieve a targeted cell recovery of 10,000 cells.

value: tissue culutre

value: NK cells

tag: time

value: Culture


title: Cec_18mCK4

tag: tissue


title: AH2Tg-1


title: Cec_8wCKM5

tag: cell type


title: B16F10_15dpi_tumor

source_name: tumor

tag: treatment

value: B16F10 tumor


title: B16F10_15dpi_spleen

source_name: spleen

value: spleen


title: WT-3

value: WT


title: WT-1


title: E0771_15dpi_tumor

value: E0771 tumor


title: WT-2


title: iWAT AH2Tg

data_processing:
Primary sequencing data was produced by Illumina HiSeqTM 2000, the original image data is transferred into sequence data via base calling (Illumina GA Pipeline v1.5), which is defined as raw data or raw reads and saved as FASTQ file.
We define "dirty" raw reads as reads which contain the sequence of adapter, high content of unknown bases and low quality reads. They need to be removed before data analysis. Filtering steps are as follows: 1) Remove reads with adapters; 2) Remove reads in which unknown bases are more than 10%; 3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more than 10).
We use BWA to map clean reads to genome reference and use Bowtie to gene reference.
The alignment data is utilized to calculate distribution of reads on reference genes and mapping ratio.
Genes and isoforms expression level are quantified by a software package: RSEM(RNASeq by Expectation Maximization). FPKM method is used in calculated expression level
Assembly: mm10
Supplementary files format and content: FPKM of each sample was provided in TXT file

extract_protocol:
Subcutaneoues white fat pad were removed, flash frozen in liquid nitrogen, and RNA was harvested using Tri-reagent
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA(for eukaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using Illumina HiSeqTM 2000 or other sequencer when necessary

value: 7 day cold exposure at 6 degreeC


title: B16F10_07dpi_tumor

value: tumor


title: Cec_18mEG4

tag: cell line


title: iWAT H2KO

tag: genotype


title: 1team-3

city: Xi’an

first: Shan

last: Huang

address: No.157, Xi Wu Road

institute: The Second Afﬁliated Hospital of Xi’an Jiaotong University

data_processing:
Agarose gel electrophoresis is used to detect the integrity of the total RNA samples.Agilent 2100 Bioanalyzer is used to assess the quality and concentration of sequencing libraries.  The NanoDrop ND-1000 is employed to measure the accurate concentration of the total RNA (abs 260) as well as protein contamination and other conditions (ratio abs260/abs230).
Quantitative analysis of gene expression is conducted at two levels: Gene Level and Transcript Level. Software such as StringTie calculates transcript abundance by aligning sequencing results to known transcriptomes.
Balgown is used for further computation, and the unit of expression quantity is represented by FPKM (Fragments Per Kilobase of transcript per Million mapped reads).
A threshold is set to screen for differentially expressed genes and transcripts, which requires a 1.5-fold difference, a p-value < 0.05, and a mean FPKM value within the group > 0.5.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Esophagus

extract_protocol:
The extracted total RNA samples are subjected to agarose electrophoresis and Nanodrop quality inspection and quantification, followed by mRNA enrichment using oligo(dT) magnetic beads.1-2 ug of total RNA was used for the construction of sequencing libraries.
Total RNA is first enriched for mRNA using the NEB Next® Poly(A) mRNA Magnetic Isolation Module (or rRNA is removed using the RiboZero Magnetic Gold Kit). The processed RNA product is then used to construct a library with the KAPA Stranded RNA-Seq Library Prep Kit (Illumina).

value: Esophagus

value: Esophageal squamous cell carcinoma

value: FGL1 overexpression